Journal of Microbiology

Journal Article

Identification of avaC from Human Gut Microbial Isolates that Converts 5AVA to 2-Piperidone.: Qiudi Zhou, Lihui Feng; J. Microbiol. 2024;62(5):367-379. Published online June 17, 2024; DOI: https://doi.org/10.1007/s12275-024-00141-0

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Abstract: 2-piperidone is a crucial industrial raw material of high-value nylon-5 and nylon-6,5. Currently, a major bottleneck in the biosynthesis of 2-piperidone is the identification of highly efficient 2-piperidone synthases. In this study, we aimed to identify specific strains among 51 human gut bacterial strains capable of producing 2-piperidone and to elucidate its synthetic mechanism. Our findings revealed that four gut bacterial strains, namely Collinsella aerofaciens LFYP39, Collinsella intestinalis LFYP54, Clostridium bolteae LFYP116, and Clostridium hathewayi LFYP18, could produce 2-piperidone from 5-aminovaleric acid (5AVA). Additionally, we observed that 2-piperidone could be synthesized from proline through cross-feeding between Clostridium difficile LFYP43 and one of the four 2-piperidone producing strains, respectively. To identify the enzyme responsible for catalyzing the conversion of 5AVA to 2-piperidone, we utilized a gain-of-function library and identified avaC (5-aminovaleric acid cyclase) in C. intestinalis LFYP54. Moreover, homologous genes of avaC were validated in the other three bacterial strains. Notably, avaC were found to be widely distributed among environmental bacteria. Overall, our research delineated the gut bacterial strains and genes involved in 2-piperidone production, holding promise for enhancing the efficiency of industrial biosynthesis of this compound.

Reviews

Application of Microbiome‑Based Therapies in Chronic Respiratory Diseases: Se Hee Lee, Jang Ho Lee, Sei Won Lee; J. Microbiol. 2024;62(3):201-216. Published online April 18, 2024; DOI: https://doi.org/10.1007/s12275-024-00124-1

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Abstract: The application of microbiome-based therapies in various areas of human disease has recently increased. In chronic respiratory disease, microbiome-based clinical applications are considered compelling options due to the limitations of current treatments. The lung microbiome is ecologically dynamic and afected by various conditions, and dysbiosis is associated with disease severity, exacerbation, and phenotype as well as with chronic respiratory disease endotype. However, it is not easy to directly modulate the lung microbiome. Additionally, studies have shown that chronic respiratory diseases can be improved by modulating gut microbiome and administrating metabolites. Although the composition, diversity, and abundance of the microbiome between the gut and lung are considerably diferent, modulation of the gut microbiome could improve lung dysbiosis. The gut microbiome infuences that of the lung via bacterial-derived components and metabolic degradation products, including short-chain fatty acids. This phenomenon might be associated with the cross-talk between the gut microbiome and lung, called gut-lung axis. There are multiple alternatives to modulate the gut microbiome, such as prebiotics, probiotics, and postbiotics ingestion and fecal material transplantation. Several studies have shown that high-fber diets, for example, present benefcial efects through the production of short-chain fatty acids. Additionally, genetically modifed probiotics to secrete some benefcial molecules might also be utilized to treat chronic respiratory diseases. Further studies on microbial modulation to regulate immunity and potentiate conventional pharmacotherapy will improve microbiome modulation techniques, which will develop as a new therapeutic area in chronic respiratory diseases.

Balancing Act of the Intestinal Antimicrobial Proteins on Gut Microbiota and Health: Ye Eun Ra, Ye‑Ji Bang; J. Microbiol. 2024;62(3):167-179. Published online April 17, 2024; DOI: https://doi.org/10.1007/s12275-024-00122-3

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Abstract: The human gut houses a diverse and dynamic microbiome critical for digestion, metabolism, and immune development, exerting profound efects on human health. However, these microorganisms pose a potential threat by breaching the gut barrier, entering host tissues, and triggering infections, uncontrolled infammation, and even sepsis. The intestinal epithelial cells form the primary defense, acting as a frontline barrier against microbial invasion. Antimicrobial proteins (AMPs), produced by these cells, serve as innate immune efectors that regulate the gut microbiome by directly killing or inhibiting microbes. Abnormal AMP production, whether insufcient or excessive, can disturb the microbiome equilibrium, contributing to various intestinal diseases. This review delves into the complex interactions between AMPs and the gut microbiota and sheds light on the role of AMPs in governing host-microbiota interactions. We discuss the function and mechanisms of action of AMPs, their regulation by the gut microbiota, microbial evasion strategies, and the consequences of AMP dysregulation in disease. Understanding these complex interactions between AMPs and the gut microbiota is crucial for developing strategies to enhance immune responses and combat infections within the gut microbiota. Ongoing research continues to uncover novel aspects of this intricate relationship, deepening our understanding of the factors shaping gut health. This knowledge has the potential to revolutionize therapeutic interventions, ofering enhanced treatments for a wide range of gut-related diseases.

Skin Deep: The Potential of Microbiome Cosmetics: Ju Hee Han, Hei Sung Kim; J. Microbiol. 2024;62(3):181-199. Published online April 16, 2024; DOI: https://doi.org/10.1007/s12275-024-00128-x

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Abstract: The interplay between the skin microbiome and its host is a complex facet of dermatological health and has become a critical focus in the development of microbiome cosmetics. The skin microbiome, comprising various microorganisms, is essential from birth, develops over the lifespan, and performs vital roles in protecting our body against pathogens, training the immune system, and facilitating the breakdown of organic matter. Dysbiosis, an imbalance of these microorganisms, has been implicated in a number of skin conditions such as acne, atopic dermatitis, and skin cancer. Recent scientific findings have spurred cosmetic companies to develop products that preserve and enhance the skin's microbial diversity balance. These products may incorporate elements like prebiotics, probiotics, and postbiotics, which are beneficial for the skin microbiome. Beyond topical products, there's increasing interest in ingestible beauty supplements (i.e. oral probiotics), highlighting the connection between the gut and skin. This review examines the influence of the microbiome on skin health and the emerging trends of microbiome skincare products.

Metabolic Interaction Between Host and the Gut Microbiota During High‑Fat Diet‑Induced Colorectal Cancer: Chaeeun Lee, Seungrin Lee, Woongjae Yoo; J. Microbiol. 2024;62(3):153-165. Published online April 16, 2024; DOI: https://doi.org/10.1007/s12275-024-00123-2

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Abstract: Colorectal cancer (CRC) is the second-highest cause of cancer-associated mortality among both men and women worldwide. One of the risk factors for CRC is obesity, which is correlated with a high-fat diet prevalent in Western dietary habits. The association between an obesogenic high-fat diet and CRC has been established for several decades; however, the mechanisms by which a high-fat diet increases the risk of CRC remain unclear. Recent studies indicate that gut microbiota strongly infuence the pathogenesis of both high-fat diet-induced obesity and CRC. The gut microbiota is composed of hundreds of bacterial species, some of which are implicated in CRC. In particular, the expansion of facultative anaerobic Enterobacteriaceae, which is considered a microbial signature of intestinal microbiota functional imbalance (dysbiosis), is associated with both high-fat diet-induced obesity and CRC. Here, we review the interaction between the gut microbiome and its metabolic byproducts in the context of colorectal cancer (CRC) during high-fat diet-induced obesity. In addition, we will cover how a high-fat diet can drive the expansion of genotoxin-producing Escherichia coli by altering intestinal epithelial cell metabolism during gut infammation conditions.

Journal Article

Hydroxychloroquine an Antimalarial Drug, Exhibits Potent Antifungal Efficacy Against Candida albicans Through Multitargeting.: Sargun Tushar Basrani, Tanjila Chandsaheb Gavandi, Shivani Balasaheb Patil, Nandkumar Subhash Kadam, Dhairyasheel Vasantrao Yadav, Sayali Ashok Chougule, Sankunny Mohan Karuppayil, Ashwini Khanderao Jadhav; J. Microbiol. 2024;62(5):381-391. Published online April 8, 2024; DOI: https://doi.org/10.1007/s12275-024-00111-6

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Abstract: Candida albicans is the primary etiological agent associated with candidiasis in humans. Unrestricted growth of C. albicans can progress to systemic infections in the worst situation. This study investigates the antifungal activity of Hydroxychloroquine (HCQ) and mode of action against C. albicans. HCQ inhibited the planktonic growth and yeast to hyphal form morphogenesis of C. albicans significantly at 0.5 mg/ml concentration. The minimum inhibitory concentrations (MIC(50)) of HCQ for C. albicans adhesion and biofilm formation on the polystyrene surface was at 2 mg/ml and 4 mg/ml respectively. Various methods, such as scanning electron microscopy, exploration of the ergosterol biosynthesis pathway, cell cycle analysis, and assessment of S oxygen species (ROS) generation, were employed to investigate HCQ exerting its antifungal effects. HCQ was observed to reduce ergosterol levels in the cell membranes of C. albicans in a dose-dependent manner. Furthermore, HCQ treatment caused a substantial arrest of the C. albicans cell cycle at the G0/G1 phase, which impeded normal cell growth. Gene expression analysis revealed upregulation of SOD2, SOD1, and CAT1 genes after HCQ treatment, while genes like HWP1, RAS1, TEC1, and CDC 35 were downregulated. The study also assessed the in vivo efficacy of HCQ in a mice model, revealing a reduction in the pathogenicity of C. albicans after HCQ treatment. These results indicate that HCQ holds for the development of novel antifungal therapies.

Review

Genomic Evolution and Recombination Dynamics of Human Adenovirus D Species: Insights from Comprehensive Bioinformatic Analysis.: Anyeseu Park, Chanhee Lee, Jeong Yoon Lee; J. Microbiol. 2024;62(5):393-407. Published online March 7, 2024; DOI: https://doi.org/10.1007/s12275-024-00112-5

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Abstract: Human adenoviruses (HAdVs) can infect various epithelial mucosal cells, ultimately causing different symptoms in infected organ systems. With more than 110 types classified into seven species (A-G), HAdV-D species possess the highest number of viruses and are the fastest proliferating. The emergence of new adenovirus types and increased diversity are driven by homologous recombination (HR) between viral genes, primarily in structural elements such as the penton base, hexon and fiber proteins, and the E1 and E3 regions. A comprehensive analysis of the HAdV genome provides valuable insights into the evolution of human adenoviruses and identifies genes that display high variation across the entire genome to determine recombination patterns. Hypervariable regions within genetic sequences correlate with functional characteristics, thus allowing for adaptation to new environments and hosts. Proteotyping of newly emerging and already established adenoviruses allows for prediction of the characteristics of novel viruses. HAdV-D species evolved in a direction that increased diversity through gene recombination. Bioinformatics analysis across the genome, particularly in highly variable regions, allows for the verification or re-evaluation of recombination patterns in both newly introduced and pre-existing viruses, ultimately aiding in tracing various biological traits such as virus tropism and pathogenesis. Our research does not only assist in predicting the emergence of new adenoviruses but also offers critical guidance in regard to identifying potential regulatory factors of homologous recombination hotspots.

Journal Articles

Effects of Feather Hydrolysates Generated by Probiotic Bacillus licheniformis WHU on Gut Microbiota of Broiler and Common carp.: Kamin Ke, Yingjie Sun, Tingting He, Wenbo Liu, Yijiao Wen, Siyuan Liu, Qin Wang, Xiaowei Gao; J. Microbiol. 2024;62(6):473-487. Published online February 29, 2024; DOI: https://doi.org/10.1007/s12275-024-00118-z

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Abstract: Due to the ever-increasing demand for meat, it has become necessary to identify cheap and sustainable sources of protein for animal feed. Feathers are the major byproduct of poultry industry, which are rich in hard-to-degrade keratin protein. Previously we found that intact feathers can be digested into free amino acids, short peptides, and nano-/micro-keratin particles by the strain Bacillus licheniformis WHU in water, and the resulting feather hydrolysates exhibit prebiotic effects on mice. To explore the potential utilization of feather hydrolysate in the feed industry, we investigated its effects on the gut microbiota of broilers and fish. Our results suggest that feather hydrolysates significantly decrease and increase the diversity of gut microbial communities in broilers and fish, respectively. The composition of the gut microbiota was markedly altered in both of the animals. The abundance of bacteria with potentially pathogenic phenotypes in the gut microbial community of the fish significantly decreased. Staphylococcus spp., Pseudomonas spp., Neisseria spp., Achromobacter spp. were significantly inhibited by the feather hydrolysates. In addition, feather hydrolysates significantly improved proteolytic activity in the guts of broilers and fish. In fish, the expression levels of ZO-1 and TGF-α significantly improved after administration of feather hydrolysates. The results presented here suggest that feather hydrolysates generated by B. licheniformis WHU could be an alternative protein source in aquaculture and could exert beneficial effects on fish.

Mycobacterium tuberculosis PE_PGRS45 (Rv2615c) Promotes Recombinant Mycobacteria Intracellular Survival via Regulation of Innate Immunity, and Inhibition of Cell Apoptosis: Tao Xu , Chutong Wang , Minying Li , Jing Wei , Zixuan He , Zhongqing Qian , Xiaojing Wang , Hongtao Wang; J. Microbiol. 2024;62(1):49-62. Published online February 9, 2024; DOI: https://doi.org/10.1007/s12275-023-00101-0

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Abstract: Tuberculosis (TB), a bacterial infectious disease caused by Mycobacterium tuberculosis (M. tuberculosis), is a significant global public health problem. Mycobacterium tuberculosis expresses a unique family of PE_PGRS proteins that have been implicated in pathogenesis. Despite numerous studies, the functions of most PE_PGRS proteins in the pathogenesis of mycobacterium infections remain unclear. PE_PGRS45 (Rv2615c) is only found in pathogenic mycobacteria. In this study, we successfully constructed a recombinant Mycobacterium smegmatis (M. smegmatis) strain which heterologously expresses the PE_PGRS45 protein. We found that overexpression of this cell wall-associated protein enhanced bacterial viability under stress in vitro and cell survival in macrophages. MS_PE_PGRS45 decreased the secretion of pro-inflammatory cytokines such as IL-1β, IL-6, IL-12p40, and TNF-α. We also found that MS_PE_PGRS45 increased the expression of the anti-inflammatory cytokine IL-10 and altered macrophage-mediated immune responses. Furthermore, PE_PGRS45 enhanced the survival rate of M. smegmatis in macrophages by inhibiting cell apoptosis. Collectively, our findings show that PE_PGRS45 is a virulent factor actively involved in the interaction with the host macrophage.

Genetic and Functional Characterization of a Salicylate 1‑monooxygenase Located on an Integrative and Conjugative Element (ICE) in Pseudomonas stutzeri AJR13: Igor Ivanovski , Gerben J. Zylstra; J. Microbiol. 2023;61(12):1025-1032. Published online December 15, 2023; DOI: https://doi.org/10.1007/s12275-023-00093-x

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Abstract: Pseudomonas stutzeri strain AJR13 was isolated for growth on the related compounds biphenyl (BPH) and diphenylmethane (DPM). The BPH and DPM degradative pathway genes are present on an integrative and conjugative element (ICE) in the chromosome. Examination of the genome sequence of AJR13 revealed a gene encoding a salicylate 1-monooxygenase (salA) associated with the ICE even though AJR13 did not grow on salicylate. Transfer of the ICE to the well-studied Pseudomonas putida KT2440 resulted in a KT2440 strain that could grow on salicylate. Knockout mutagenesis of the salA gene on the ICE in KT2440 eliminated the ability to grow on salicylate. Complementation of the knockout with the cloned salA gene restored growth on salicylate. Transfer of the cloned salA gene under control of the lac promoter to KT2440 resulted in a strain that could grow on salicylate. Heterologous expression of the salA gene in E. coli BL21 DE3 resulted in the production of catechol from salicylate, confirming that it is indeed a salicylate 1-monooxygenase. Interestingly, transfer of the cloned salA gene under control of the lac promoter to AJR13 resulted in a strain that could now grow on salicylate, suggesting that gene expression for the downstream catechol pathway is intact.

Quantitative Analysis of RNA Polymerase Slippages for Production of P3N‑PIPO Trans‑frame Fusion Proteins in Potyvirids: Dongjin Choi , Yoonsoo Hahn; J. Microbiol. 2023;61(10):917-927. Published online October 16, 2023; DOI: https://doi.org/10.1007/s12275-023-00083-z

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Abstract: Potyvirids, members of the family Potyviridae, produce the P3N-PIPO protein, which is crucial for the cell-to-cell transport of viral genomic RNAs. The production of P3N-PIPO requires an adenine (A) insertion caused by RNA polymerase slippage at a conserved GAA AAA A ( GA6) sequence preceding the PIPO open reading frame. Presently, the slippage rate of RNA polymerase has been estimated in only a few potyvirids, ranging from 0.8 to 2.1%. In this study, we analyzed publicly available plant RNA-seq data and identified 19 genome contigs from 13 distinct potyvirids. We further investigated the RNA polymerase slippage rates at the GA6 motif. Our analysis revealed that the frequency of the A insertion variant ranges from 0.53 to 4.07% in 11 potyviruses (genus Potyvirus). For the two macluraviruses (genus Macluravirus), the frequency of the A insertion variant was found to be 0.72% and 10.96% respectively. Notably, the estimated RNA polymerase slippage rates for 12 out of the 13 investigated potyvirids were reported for the first time in this study. Our findings underscore the value of plant RNA-seq data for quantitative analysis of potyvirid genome variants, specifically at the GA6 slippage site, and contribute to a more comprehensive understanding of the RNA polymerase slippage phenomenon in potyvirids.

Mycorrhizal Fungal Diversity Associated with Six Understudied Ectomycorrhizal Trees in the Republic of Korea: Ki Hyeong Park , Seung-Yoon Oh , Yoonhee Cho , Chang Wan Seo , Ji Seon Kim , Shinnam Yoo , Jisun Lim , Chang Sun Kim , Young Woon Lim; J. Microbiol. 2023;61(8):729-739. Published online September 4, 2023; DOI: https://doi.org/10.1007/s12275-023-00073-1

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Abstract: Mycorrhizal fungi are key components of forest ecosystems and play essential roles in host health. The host specificity of mycorrhizal fungi is variable and the mycorrhizal fungi composition for the dominant tree species is largely known but remains unknown for the less common tree species. In this study, we collected soil samples from the roots of six understudied ectomycorrhizal tree species from a preserved natural park in the Republic of Korea over four seasons to investigate the host specificity of mycorrhizal fungi in multiple tree species, considering the abiotic factors. We evaluated the mycorrhizal fungal composition in each tree species using a metabarcoding approach. Our results revealed that each host tree species harbored unique mycorrhizal communities, despite close localization. Most mycorrhizal taxa belonged to ectomycorrhizal fungi, but a small proportion of ericoid mycorrhizal fungi and arbuscular mycorrhizal fungi were also detected. While common mycorrhizal fungi were shared between the plant species at the genus or higher taxonomic level, we found high host specificity at the species/OTU (operational taxonomic unit) level. Moreover, the effects of the seasons and soil properties on the mycorrhizal communities differed by tree species. Our results indicate that mycorrhizal fungi feature host-specificity at lower taxonomic levels.

Chemokine CCL6 Plays Key Role in the Inhibitory Effect of Vitamin A on Norovirus Infection: Heetae Lee , Giljae Lee , You-Hee Cho , Youngcheon Song , GwangPyo Ko; J. Microbiol. 2023;61(5):579-587. Published online May 26, 2023; DOI: https://doi.org/10.1007/s12275-023-00047-3

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Abstract: Norovirus (NoV) is the most common viral cause of acute gastroenteritis worldwide. Vitamin A has demonstrated the potential to protect against gastrointestinal infections. However, the effects of vitamin A on human norovirus (HuNoV) infections remain poorly understood. This study aimed to investigate how vitamin A administration affects NoV replication. We demonstrated that treatment with retinol or retinoic acid (RA) inhibited NoV replication in vitro based on their effects on HuNoV replicon-bearing cells and murine norovirus-1 (MNV-1) replication in murine cells. MNV replication in vitro showed significant transcriptomic changes, which were partially reversed by retinol treatment. RNAi knockdown of CCL6, a chemokine gene that was downregulated by MNV infection but upregulated by retinol administration, resulted in increased MNV replication in vitro. This suggested a role of CCL6 in the host response to MNV infections. Similar gene expression patterns were observed in the murine intestine after oral administration of RA and/or MNV-1.CW1. CCL6 directly decreased HuNoV replication in HG23 cells, and might indirectly regulate the immune response against NoV infection. Finally, relative replication levels of MNV-1.CW1 and MNV-1.CR6 were significantly increased in CCL6 knockout RAW 264.7 cells. This study is the first to comprehensively profile transcriptomes in response to NoV infection and vitamin A treatment in vitro, and thus may provide new insights into dietary prophylaxis and NoV infections.

Epidemiological Characteristics of Norovirus Outbreaks in Shenyang from 2017 to 2021: Ying Qi , Xinxin Dong , Xiaowei Cheng , Han Xu , Jin Wang , Bing Wang , Ye Chen , Baijun Sun , Linlin Zhang , Yan Yao; J. Microbiol. 2023;61(4):471-478. Published online March 27, 2023; DOI: https://doi.org/10.1007/s12275-023-00033-9

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Abstract: Norovirus is one of the leading causes of acute gastroenteritis outbreaks worldwide. This study aimed to identify the epidemiological characteristics of norovirus outbreaks and to provide evidence for public health entities. Specimens and epidemiological survey data were collected to determine if there were differences in the attack rate of norovirus in terms of the year, season, transmission route, exposure setting, and region and to determine whether there were relationships between the reporting interval, the number of illnesses in a single outbreak and the duration of the outbreak. Norovirus outbreaks were reported throughout the year, with seasonal characteristics (i.e., high rates in spring and winter). Among all regions in Shenyang with the exception of Huanggu and Liaozhong, norovirus outbreaks had been reported, and the primary genotype was GII.2[P16]. Vomiting was the most common symptom. The main places of occurrence were childcare institutions and schools. The person-to-person route was the main transmission route. The median duration of norovirus was 3 days (IQR [interquartile range]: 2–6 days), the median reporting interval was 2 days (IQR: 1–4 days), the median number of illnesses in a single outbreak was 16 (IQR: 10–25); there was a positive correlation between these parameters. Norovirus surveillance and genotyping studies still need to be further strengthened to increase knowledge regarding the pathogens and their variant characteristics, to better characterize the patterns of norovirus outbreaks and to provide information for outbreak prevention. Norovirus outbreaks should be detected, reported and handled early. Public health entities and the government should develop corresponding measures for different seasons, transmission routes, exposure settings, and regions.

CXCL12/CXCR4 Axis is Involved in the Recruitment of NK Cells by HMGB1 Contributing to Persistent Airway Inflammation and AHR During the Late Stage of RSV Infection: Sisi Chen , Wei Tang , Guangyuan Yu , Zhengzhen Tang , Enmei Liu; J. Microbiol. 2023;61(4):461-469. Published online February 13, 2023; DOI: https://doi.org/10.1007/s12275-023-00018-8

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Abstract: We previously showed that both high-mobility group box-1 (HMGB1) and natural killer (NK) cells contribute to respiratory syncytial virus (RSV)-induced persistent airway inflammation and airway hyperresponsiveness (AHR). Meanwhile, Chemokine (C-X-C motif) ligand 12 (CXCL12) and its specific receptor (chemokine receptor 4, CXCR4) play important roles in recruitment of immune cells. CXCL12 has been reported to form a complex with HMGB1 that binds to CXCR4 and increases inflammatory cell migration. The relationship between HMGB1, NK cells and chemokines in RSV-infected model remains unclear. An anti-HMGB1 neutralizing antibody and inhibitor of CXCR4 (AMD3100) was administered to observe changes of NK cells and airway disorders in nude mice and BALB/c mice. Results showed that the mRNA expression and protein levels of HMGB1 were elevated in late stage of RSV infection and persistent airway inflammation and AHR were diminished after administration of anti-HMGB1 antibodies, with an associated significant decrease in CXCR4+ NK cells. In addition, CXCL12 and CXCR4 were reduced after HMGB1 blockade. Treatment with AMD3100 significantly suppressed the recruitment of NK cells and alleviated the airway disorders. Thus, CXCL12/CXCR4 axis is involved in the recruitment of NK cells by HMGB1, contributing to persistent airway inflammation and AHR during the late stage of RSV infection.

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